annotate data_manager/bwa_mem_index_builder.xml @ 8:63d5652be07a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"

<tool id="bwa_mem_index_builder_data_manager" name="BWA-MEM index" tool_type="manage_data" version="0.0.5" profile="19.05">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="0.7.17">bwa</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/bwa_mem_index_builder.py'
        '${out_file}'
        --fasta_filename '${all_fasta_source.fields.path}'
        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
        --fasta_description '${all_fasta_source.fields.name}'
        --data_table_name bwa_mem_indexes
    ]]></command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="sequence_name" type="text" value="" label="Name of sequence" />
        <param name="sequence_id" type="text" value="" label="ID for sequence" />

        <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index">
            <option value="automatic" selected="true">Guess automatically (2GB cut-off)</option>
            <option value="is">IS linear-time algorithm (for small genomes)</option>
            <option value="bwtsw">BWT-SW (for large genomes)</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <output name="out_file" value="bwa_mem_data_manager.json"/>
        </test>
    </tests>
    <help>
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>